Variant report

Variant	rs1427577
Chromosome Location	chr7:124985986-124985987
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPAM1-9	chr7:124985879-124986251	NONHSAT123107

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10227101	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10255880	0.94[EUR][1000 genomes]
rs10500105	0.99[ASN][1000 genomes]
rs11981796	0.91[EUR][1000 genomes]
rs12706650	0.92[EUR][1000 genomes]
rs13307715	0.90[ASN][1000 genomes]
rs1346368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1427578	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1427581	0.99[ASN][1000 genomes]
rs17148212	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17331251	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17390435	0.99[ASN][1000 genomes]
rs1820593	0.87[ASN][1000 genomes]
rs1896471	0.82[EUR][1000 genomes]
rs28667732	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34184477	0.99[ASN][1000 genomes]
rs34330657	0.90[ASN][1000 genomes]
rs34574207	0.99[ASN][1000 genomes]
rs35038175	0.99[ASN][1000 genomes]
rs35074599	0.88[ASN][1000 genomes]
rs35275809	0.97[ASN][1000 genomes]
rs35552657	0.90[ASN][1000 genomes]
rs35573480	0.90[ASN][1000 genomes]
rs36103965	0.99[ASN][1000 genomes]
rs58600715	0.83[ASN][1000 genomes]
rs61518741	0.90[ASN][1000 genomes]
rs62477097	0.83[ASN][1000 genomes]
rs62481756	0.90[ASN][1000 genomes]
rs62482063	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6467001	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6467002	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6948950	1.00[ASN][1000 genomes]
rs6958411	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6964687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6965492	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs6970401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6973477	0.99[ASN][1000 genomes]
rs6973838	0.99[ASN][1000 genomes]
rs7780337	0.99[ASN][1000 genomes]
rs7787379	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7795867	0.99[ASN][1000 genomes]
rs7804055	0.99[ASN][1000 genomes]
rs9692521	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422188	chr7:124782873-125254203	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv2761087	chr7:124823624-125429662	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv889140	chr7:124921028-125042024	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv464709	chr7:124921028-125068580	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv608345	chr7:124921028-125068580	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv889141	chr7:124935779-125072969	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv889142	chr7:124958806-125068580	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv608346	chr7:124962085-124996787	Enhancers Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1028369	chr7:124967804-125508233	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv948720	chr7:124970772-125783434	Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv889143	chr7:124977736-125042024	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv889144	chr7:124977736-125068580	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv889145	chr7:124977736-125231999	Enhancers ZNF genes & repeats Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv970937	chr7:124985881-124986592	Enhancers	lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:1 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:124985800-124986400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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